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- EMDB-3045: Density map of the scanning state of the mammalian SRP-ribosome c... -

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Basic information

Entry
Database: EMDB / ID: EMD-3045
TitleDensity map of the scanning state of the mammalian SRP-ribosome complex
Map dataThis is the final masked and sharpened reconstruction
Sample
  • Sample: Complex of the mammalian ribosome and SRP in its scanning mode
  • Complex: Mammalian ribosome
  • RNA: Signal recognition particle
Keywordsribosomes / SRP / mammal / translocation
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsVoorhees RM / Hegde RS
CitationJournal: Elife / Year: 2015
Title: Structures of the scanning and engaged states of the mammalian SRP-ribosome complex.
Authors: Rebecca M Voorhees / Ramanujan S Hegde /
Abstract: The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially ...The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, and delivers these ribosome-nascent chain complexes to the membrane. Here, we present structures of native mammalian SRP-ribosome complexes in the scanning and engaged states. These structures reveal the near-identical SRP architecture of these two states, show many of the SRP-ribosome interactions at atomic resolution, and suggest how the polypeptide-binding M domain selectively engages hydrophobic signals. The scanning M domain, pre-positioned at the ribosomal exit tunnel, is auto-inhibited by a C-terminal amphipathic helix occluding its hydrophobic binding groove. Upon engagement, the hydrophobic targeting signal displaces this amphipathic helix, which then acts as a protective lid over the signal. Biochemical experiments suggest how scanning and engagement are coordinated with translation elongation to minimize exposure of hydrophobic signals during membrane targeting.
History
DepositionJun 15, 2015-
Header (metadata) releaseAug 12, 2015-
Map releaseAug 12, 2015-
UpdateAug 12, 2015-
Current statusAug 12, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jan
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3045.png

Downloads & links

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Map

FileDownload / File: emd_3045.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the final masked and sharpened reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 420 pix.
= 562.8 Å		1.34 Å/pix.
x 420 pix.
= 562.8 Å		1.34 Å/pix.
x 420 pix.
= 562.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.38412941 - 0.57654124
Average (Standard dev.)0.00115846 (±0.01818872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 562.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z562.800562.800562.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.3840.5770.001

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Supplemental data

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Supplemental map: emd 3045 half map 1.map

Fileemd_3045_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 3045 half map 2.map

Fileemd_3045_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the mammalian ribosome and SRP in its scanning mode

EntireName: Complex of the mammalian ribosome and SRP in its scanning mode
Components
  • Sample: Complex of the mammalian ribosome and SRP in its scanning mode
  • Complex: Mammalian ribosome
  • RNA: Signal recognition particle

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Supramolecule #1000: Complex of the mammalian ribosome and SRP in its scanning mode

SupramoleculeName: Complex of the mammalian ribosome and SRP in its scanning mode
type: sample / ID: 1000 / Oligomeric state: Heterodimer of mammalian ribosome and SRP / Number unique components: 2

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Supramolecule #1: Mammalian ribosome

SupramoleculeName: Mammalian ribosome / type: complex / ID: 1 / Name.synonym: 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Cell: reticulocyte

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Macromolecule #1: Signal recognition particle

MacromoleculeName: Signal recognition particle / type: rna / ID: 1 / Name.synonym: SRP / Details: ribonucleoprotein complex / Classification: OTHER / Structure: OTHER / Synthetic?: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 50 mM HEPES pH 7.5, 200 mM 469 KAc, 15 mM MgAc2, and 1 mM DTT
GridDetails: glow-discharged holey carbon grids (Quantifoil R2/2), coated with a ~70 angstrom thick layer of amorphous carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Method: sample was applied to the grid, followed by a 30 s incubation at 4C, 3 s of blotting

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateNov 14, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 27 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using the automated particle picker in Relion
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: OTHER / Software - Name: Relion
Details: Final maps were calculated from two averaged data sets
Number images used: 27627

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